About 3D Slicer¶
What is 3D Slicer?¶
- A software application for visualization and analysis of medical image computing data sets. All commonly used data sets are supported, such as images, segmentations, surfaces, annotations, transformations, etc., in 2D, 3D, and 4D. Visualization is available on desktop and in virtual reality. Analysis includes segmentation, registration, and various quantifications.
- A research software platform, which allows researchers to quickly develop and evaluate new methods and distribute them to clinical users. All features are available and extensible in Python and C++. A full Python environment is provided where any Python packages can be installed and combined with built-in features. Slicer has a built-in Python console and can act as a Jupyter notebook kernel with remote 3D rendering capabilities.
- Product development platform, which allows companies to quickly prototype and release products to users. Developers can focus on developing new methods and do not need to spend time with redeveloping basic data import/export, visualization, interaction features. The application is designed to be highly customizable (with custom branding, simplified user interface, etc.). 3D Slicer is completely free and there are no restrictions on how it is used - it is up to the software distributor to ensure that the developed application is suitable for the intended use.
Note: There is no restriction on use, but Slicer is NOT approved for clinical use and the distributed application is intended for research use. Permissions and compliance with applicable rules are the responsibility of the user. For details on the license see here.
- Free, open-source software available on multiple operating systems: Linux, MacOSX and Windows.
- Multi organ: from head to toe.
- Support for multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy.
- Real-time interface for medical devices, such as surgical navigation systems, imaging systems, robotic devices, and sensors.
- Highly extensible: users can easily add more capabilities by installing additional modules from the Extensions manager, running custom Python scripts in the built-in Python console, run any executables from the application’s user interface, or implement custom modules in Python or C++.
- Large and active user community.
The 3D Slicer software is distributed under a BSD-style open source license that is compatible with the Open Source Definition by The Open Source Initiative and contains no restrictions on use of the software.
To use Slicer, please read the 3D Slicer Software License Agreement before downloading any binary releases of the Slicer.
How to cite¶
3D Slicer as a platform¶
To acknowledge 3D Slicer as a platform, please cite the Slicer web site and the following publications when publishing work that uses or incorporates 3D Slicer:
Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network. Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.
To acknowledge individual modules: each module has an acknowledgment tab in the top section. Information about contributors and funding source can be found there:
Additional information (including information about the underlying publications) can be typically found on the manual pages accessible through the help tab in the top section:
Slicer is made possible through contributions from an international community of scientists from a multitude of fields, including engineering and biomedicine. The following sections give credit to some of the major contributors to the 3D Slicer core effort. Each 3D Slicer extension has a separate acknowledgements page with information specific to that extension.
Ongoing Slicer support depends on YOU
Please give the Slicer repository a star on github. This is an easy way to show thanks and it can help us qualify for useful services that are only open to widely recognized open projects. Don’t forget to cite our publications because that helps us get new grant funding. If you find Slicer is helpful like the community please get involved. You don’t need to be a programmer to help!
- Ron Kikinis: Principal Investigator
- Steve Pieper: Chief Architect
- Jean-Christophe Fillion-Robin: Lead Developer
- Nicole Aucoin
- Stephen Aylward
- Andrey Fedorov
- Noby Hata
- Hans Johnson
- Tina Kapur
- Gabor Fichtinger
- Andras Lasso
- Csaba Pinter
- Jim Miller
- Sonia Pujol: Director of Training
- Junichi Tokuda
- Lauren O’Donnell
- Andinet Enquobahrie
- Beatriz Paniagua
Contributors are not only developers, but also individual helping to secure funding and move the platform forward.
Groups Contributing to the Core Engineering of Slicer in a Major Way¶
- SPL: Ron Kikinis, Nicole Aucoin, Lauren O’Donnell, Andrey Fedorov, Isaiah Norton, Sonia Pujol, Noby Hata, Junichi Tokuda
- Isomics: Steve Pieper, Alex Yarmarkovich
- Kitware: Jean-Christophe Fillion-Robin, Julien Finet, Will Schroeder, Stephen Aylward, Andinet Enquobahrie, Beatriz Paniagua, Matt McCormick, Johan Andruejol, Max Smolens, Alexis Girault, Sam Horvath
- University of Iowa: Hans Johnson
- GE: Jim Miller
- Perk Lab, Queen’s University: Andras Lasso, Tamas Ungi, Csaba Pinter, Gabor Fichtinger
- Kapteyn Astronomical Institute, University of Groningen: Davide Punzo
We invite commercial entities to use 3D Slicer.
Slicer’s License makes Commercial Use Available¶
- 3D Slicer is a Free Open Source Software distributed under a BSD style license.
- The license does not impose restrictions on the use of the software.
- 3D Slicer is NOT FDA approved. It is the users responsibility to ensure compliance with applicable rules and regulations.
- For details, please see the 3D Slicer Software License Agreement.
- Ebatinca SL is an international technology company in Las Palmas, Spain focused on technology for sustainable development.
- Isomics uses 3D Slicer in a variety of academic and commercial research partnerships in fields such as planning and guidance for neurosurgery, quantitative imaging for clinical trials, clinical image informatics.
- Kitware Integral to continuing to support the 3D Slicer community, Kitware is also offering consulting services in response to the rapidly growing demand for the development of proprietary applications and commercial products based on 3D Slicer. Kitware has used 3D Slicer to rapidly prototype solutions in nearly every aspect of medical imaging and is also collaborating on the development of commercial pre-clinical and clinical products based on 3D Slicer.
- Pixel Medical builds on and contributes to 3D Slicer to develop innovative medical software from idea to clinical prototype to finished product, and to support academic research projects. Areas of expertise include radiation therapy, image guided therapy, virtual & augmented reality, hardware & device support, and machine learning & artificial intelligence.
Listed in alphabetical order.
3D Slicer based products¶
Many companies prefer not to disclose what software components they use in their products, therefore here we can only list a few commercial products that are based on 3D Slicer:
- Allen Institute for Brain Science: Cell Locator, Desktop application for manually aligning specimens to annotated 3D spaces.
- Radiopharmaceutical Imaging and Dosimetry: RPTDose, a 3D Slicer-based application that streamlines and integrates quantitative imaging analysis and dose estimation techniques to guide and optimize the use of radiopharmaceutical therapy agents in clinical trials. See more information on this Kitware blog.
- SonoVol is developing a whole-body ultrasound imaging system for small animals. This start-up company arose from research in the Department of Biomedical Engineering at the University of North Carolina at Chapel Hill. See more information on this Kitware blog.
- Xoran Technologies: Image-guided Platform for Deep Brain Stimulation Surgery 1. See more information on this Kitware blog.
- Xstrahl is developing a Small Animal Radiation Research Platform (SARRP) that uses 3D Slicer as its front-end application for radiation therapy beam placement and system control. See more information on this Kitware blog.
Listed in alphabetical order.